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SRX13463414: Xhv_ICMP4165
1 ILLUMINA (Illumina MiSeq) run: 353,697 spots, 112.5M bases, 60.1Mb downloads

Design: DNA extraction was performed using the Qiagen DNeasy UltraClean Microbial Kit (cat. no. 12224; Valencia, CA) according to the manufacturers instructions, with the following change: 5 replicates were completed for each strain, and after eluting each first replicate, that elute was used to elute the next replicate, and so on. This resulted in >2.0 ug of total DNA per strain, as measured using the ThermoFischer Qubit Fluorometer 3.0 and the Invitrogen dsDNA Broad Range Assay Kit (cat nos. Q33216 and Q32850; Waltham, MA). Library preparation and 250 x 250 paired-end whole genome sequencing was performed at the Pennsylvania State University Genomics Facility using the TruSeq DNA PCR Free Library Construction and the Illumina MiSeq System (cat. nos. FC-121-3001 and SY-410-1003; San Diego, CA).
Submitted by: The Pennsylvania State University
Study: Comparative genomic analysis of the lettuce bacterial leaf spot pathogen to investigate race specificity
show Abstracthide Abstract
Bacterial leaf spot (BLS) of lettuce caused by Xanthomonas hortorum pv. vitians (Xhv) was first described over 100 years ago and remains a significant threat to lettuce cultivation today. This study investigated the genetic relatedness of the Xhv strains and the possible genetic sources of this race-specific pathogenicity. Whole genome sequences of eighteen Xhv strains representing the three hypothesized races, along with eight related Xanthomonas strains, were included in the analysis. A maximum likelihood phylogeny based on concatenated whole genome SNPs confirmed previous results describing two major lineages of Xhv strains. Gene clusters encoding secretion systems, secondary metabolites, and bacteriocins were assessed to identify putative virulence factors that distinguish the Xhv races. Genome sequences were mined for effector genes, which have been shown to be involved in race-specificity in other systems.
Sample:
SAMN24251541 • SRS11360878 • All experiments • All runs
Library:
Name: ICMP 4165
Instrument: Illumina MiSeq
Strategy: WGS
Source: GENOMIC
Selection: unspecified
Layout: PAIRED
Runs: 1 run, 353,697 spots, 112.5M bases, 60.1Mb
Run# of Spots# of BasesSizePublished
SRR17286027353,697112.5M60.1Mb2021-12-21

ID:
18655241

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